GOLM2

Summary

GOLM2 (golgi membrane protein 2, HGNC:24892) is a protein-coding gene on chromosome 15q15.3, encoding Protein GOLM2 (Q6P4E1).

The increased expression level of this gene is associated with HER-2/neu proto-oncogene overexpression. Amplification and resulting overexpression of this proto-oncogene are found in approximately 30% of human breast and 20% of human ovarian cancers. Alternatively spliced variants encoding different isoforms have been identified for this gene.

Source: NCBI Gene 113201 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_138423

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24892
Approved symbol	GOLM2
Name	golgi membrane protein 2
Location	15q15.3
Locus type	gene with protein product
Status	Approved
Aliases	H63, DKFZp459F1927
Ensembl gene	ENSG00000166734
Ensembl biotype	protein_coding
Entrez	113201

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 16 protein_coding, 4 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000299957, ENST00000345795, ENST00000429162, ENST00000557945, ENST00000558735, ENST00000558847, ENST00000559037, ENST00000559151, ENST00000559222, ENST00000559550, ENST00000561305, ENST00000650436, ENST00000892422, ENST00000892423, ENST00000892424, ENST00000892425, ENST00000892426, ENST00000892427, ENST00000892428, ENST00000892429, ENST00000915850, ENST00000951963

RefSeq mRNA: 2 — MANE Select: NM_138423 NM_138423, NM_177974

CCDS: CCDS10108, CCDS10109

Canonical transcript exons

ENST00000299957 — 10 exons

Exon	Start	End
ENSE00001800128	44402887	44403054
ENSE00001832556	44413336	44415758
ENSE00003494874	44322965	44323019
ENSE00003506687	44379690	44379788
ENSE00003532254	44331988	44332078
ENSE00003535592	44380806	44380976
ENSE00003596613	44337763	44337907
ENSE00003666176	44328685	44328787
ENSE00003666441	44338237	44338317
ENSE00003849282	44288719	44289356

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 99.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.3636 / max 976.9348, expressed in 1814 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
146361	29.9842	1806
146364	11.7385	1712
146362	2.2843	1207
146367	0.9507	321
146365	0.4918	207
146366	0.4583	188
146363	0.4559	237

Top tissues by expression

265 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	99.28	gold quality
epithelial cell of pancreas	CL:0000083	98.82	gold quality
colonic epithelium	UBERON:0000397	98.51	gold quality
nasal cavity epithelium	UBERON:0005384	98.40	gold quality
germinal epithelium of ovary	UBERON:0001304	98.25	gold quality
adrenal tissue	UBERON:0018303	98.20	gold quality
ileal mucosa	UBERON:0000331	98.18	gold quality
bronchial epithelial cell	CL:0002328	98.14	gold quality
bronchus	UBERON:0002185	98.03	gold quality
palpebral conjunctiva	UBERON:0001812	98.00	gold quality
eye	UBERON:0000970	97.97	gold quality
Brodmann (1909) area 23	UBERON:0013554	97.93	gold quality
pigmented layer of retina	UBERON:0001782	97.92	gold quality
retina	UBERON:0000966	97.89	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.85	gold quality
endothelial cell	CL:0000115	97.75	gold quality
kidney epithelium	UBERON:0004819	97.61	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.56	gold quality
seminal vesicle	UBERON:0000998	97.50	gold quality
caput epididymis	UBERON:0004358	97.50	gold quality
lateral globus pallidus	UBERON:0002476	97.37	gold quality
skin of hip	UBERON:0001554	97.34	gold quality
epithelium of mammary gland	UBERON:0003244	97.34	gold quality
mammary duct	UBERON:0001765	97.33	gold quality
ventricular zone	UBERON:0003053	97.30	gold quality
islet of Langerhans	UBERON:0000006	97.15	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.07	gold quality
nasal cavity mucosa	UBERON:0001826	97.00	gold quality
layer of synovial tissue	UBERON:0007616	96.97	gold quality
tibia	UBERON:0000979	96.92	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7606	no	3482.58
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

130 targeting GOLM2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057

Literature-anchored findings (GeneRIF, showing 4)

• In spite of missing correlation between survival and her-2/ neu overexpression in our study, the predictive value of the her-2/ neu protooncogene in adjuvant therapy in OSCC needs further investigation. (PMID:12764679)
• Of 62 analyzed specimens, 43 tumors were HER2/neu negative compared to 19 HER2/neu positive tumors. Kaplan-Meier analysis indicated no difference in survival according to HER2/neu expression (p = 0.31, log-rank test = 1.10 (PMID:12845212)
• Shedding of cancer susceptibility candidate 4 by the convertases PC7/furin unravels a novel secretory protein implicated in cancer progression. (PMID:32820145)
• Tn antigen promotes breast cancer metastasis via impairment of CASC4. (PMID:37493437)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	golm2	ENSDARG00000074490
mus_musculus	Golm2	ENSMUSG00000060227
rattus_norvegicus	Golm2	ENSRNOG00000016357

Paralogs (1): GOLM1 (ENSG00000135052)

Protein

Protein identifiers

Protein GOLM2 — Q6P4E1 (reviewed: Q6P4E1)

Alternative names: Cancer susceptibility candidate gene 4 protein, Golgi membrane protein 2

All UniProt accessions (6): A0A3B3IRW9, Q6P4E1, H0YKJ7, H0YM51, H0YMR0, H0YN36

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the GOLM family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q6P4E1-4	4	yes
Q6P4E1-2	2
Q6P4E1-3	3
Q6P4E1-5	5

RefSeq proteins (2): NP_612432, NP_816929 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026139	GOLM1/CASC4	Family

UniProt features (22 total): modified residue 6, compositionally biased region 5, splice variant 4, topological domain 2, chain 1, transmembrane region 1, sequence conflict 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P4E1-F1	66.87	0.39

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6): 1, 233, 275, 328, 332, 366

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 162 (showing top): GCM_MAP4K4, AP4_Q6, CAGCTG_AP4_Q5, WTGAAAT_UNKNOWN, RFX1_02, FOXJ2_02, TGCCTTA_MIR124A, AP4_01, ATGTACA_MIR493, GCM_IL6ST, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, GCM_RAB10, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_DN, CTTTGCA_MIR527, GSE14415_INDUCED_TREG_VS_FOXP3_KO_INDUCED_TREG_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

714 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLM2	CDV3	Q9UKY7	506
GOLM2	CASC3	O15234	496
GOLM2	TBC1D25	Q3MII6	488
GOLM2	SPRYD3	Q8NCJ5	484
GOLM2	TMED2	Q15363	483
GOLM2	CCDC134	Q9H6E4	462
GOLM2	GOLT1B	Q9Y3E0	442
GOLM2	GTPBP10	A4D1E9	434
GOLM2	SEC23A	Q15436	410
GOLM2	SERP1	Q9Y6X1	410
GOLM2	NARF	Q9UHQ1	406
GOLM2	PMIS2	A0A1W2PS18	400
GOLM2	ZNF671	Q8TAW3	377
GOLM2	DNAI7	Q6TDU7	370
GOLM2	CDA	P32320	369

IntAct

28 interactions, top by confidence:

A	B	Type	Score
PTPN1	GOLIM4	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
GRAMD2B	EFCAB14	psi-mi:“MI:0914”(association)	0.530
BSG	BTAF1	psi-mi:“MI:0914”(association)	0.530
CHRNA4	FZD6	psi-mi:“MI:0914”(association)	0.530
GOLM2	PDIA6	psi-mi:“MI:0915”(physical association)	0.400
GSK3B	GOLM2	psi-mi:“MI:0915”(physical association)	0.370
	TMEM223	psi-mi:“MI:0914”(association)	0.350
M	DENND11	psi-mi:“MI:0914”(association)	0.350
PTPN2	GOLIM4	psi-mi:“MI:0914”(association)	0.350
CANX	HLA-A	psi-mi:“MI:0914”(association)	0.350
TMED10	PGRMC1	psi-mi:“MI:0914”(association)	0.350
IGHM	ESYT2	psi-mi:“MI:0914”(association)	0.350
CHRNA4	TMEM223	psi-mi:“MI:0914”(association)	0.350
SAAL1	QSOX1	psi-mi:“MI:0914”(association)	0.350
SYNC	NDC80	psi-mi:“MI:0914”(association)	0.350
GOLM2	EIF2B2	psi-mi:“MI:0914”(association)	0.350
BSCL2	QSOX1	psi-mi:“MI:0914”(association)	0.350
NPTN	RIMOC1	psi-mi:“MI:0914”(association)	0.350
SAAL1	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC30A1	PSMD11	psi-mi:“MI:0914”(association)	0.350
SLC30A10	GOLIM4	psi-mi:“MI:0914”(association)	0.350
SLC30A5	NBAS	psi-mi:“MI:0914”(association)	0.350
SLC39A4	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC7A1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (57): CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-RNA), CASC4 (Affinity Capture-RNA), CASC4 (Affinity Capture-MS), CASC4 (Affinity Capture-RNA), CASC4 (Two-hybrid), CASC4 (Two-hybrid), CASC4 (Two-hybrid), CASC4 (Two-hybrid), CASC4 (Two-hybrid)

ESM2 similar proteins: A2AM05, A2BDC9, A2VD12, A2VE10, A5D8S1, B1AJZ9, O00461, O75071, P04233, P04441, P07106, P10247, P24054, P70663, Q08D19, Q14515, Q32N32, Q4KLH6, Q4V9H3, Q5BJK8, Q5PQS2, Q5R5X4, Q5R6R3, Q5R8Y4, Q5R9L2, Q5T8D3, Q5TB80, Q5ZHQ6, Q5ZKQ5, Q5ZM60, Q640L3, Q6P2L7, Q6P4E1, Q6Y685, Q6ZQ06, Q70YC5, Q86TE4, Q8BG89, Q8BMK4, Q8BVV7

Diamond homologs: A2VE10, Q32N32, Q5R5X4, Q5ZKQ5, Q6P2L7, Q6P4E1, Q8NBJ4, Q91XA2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

62 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1997 predictions. Top by Δscore:

Variant	Effect	Δscore
15:44289353:CAAG:C	donor_gain	1.0000
15:44289354:AAG:A	donor_gain	1.0000
15:44289354:AAGG:A	donor_loss	1.0000
15:44289355:AG:A	donor_gain	1.0000
15:44289356:GG:G	donor_gain	1.0000
15:44289357:G:GG	donor_gain	1.0000
15:44323017:AGGG:A	donor_loss	1.0000
15:44323018:GG:G	donor_gain	1.0000
15:44323018:GGGTA:G	donor_loss	1.0000
15:44323019:GG:G	donor_gain	1.0000
15:44323020:GTAAG:G	donor_loss	1.0000
15:44323021:T:TC	donor_loss	1.0000
15:44328662:T:TA	acceptor_gain	1.0000
15:44328670:A:AG	acceptor_gain	1.0000
15:44328670:ACCTT:A	acceptor_gain	1.0000
15:44328671:C:G	acceptor_gain	1.0000
15:44328674:T:TA	acceptor_gain	1.0000
15:44328675:G:A	acceptor_gain	1.0000
15:44328678:T:TA	acceptor_gain	1.0000
15:44337761:A:AG	acceptor_gain	1.0000
15:44337762:G:GG	acceptor_gain	1.0000
15:44337762:GCAA:G	acceptor_gain	1.0000
15:44337904:A:T	donor_gain	1.0000
15:44337904:AAAG:A	donor_loss	1.0000
15:44337906:AGGTA:A	donor_loss	1.0000
15:44337907:GG:G	donor_loss	1.0000
15:44337908:GT:G	donor_loss	1.0000
15:44337909:T:A	donor_loss	1.0000
15:44338227:ACTTG:A	acceptor_gain	1.0000
15:44338230:T:TA	acceptor_gain	1.0000

AlphaMissense

2903 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:44402969:C:A	N385K	1.000
15:44402969:C:G	N385K	1.000
15:44402993:G:C	K393N	1.000
15:44402993:G:T	K393N	1.000
15:44402996:G:C	Q394H	1.000
15:44402996:G:T	Q394H	1.000
15:44403004:T:A	L397Q	1.000
15:44403004:T:C	L397P	1.000
15:44402949:T:C	Y379H	0.999
15:44402977:A:T	E388V	0.999
15:44402983:A:G	E390G	0.999
15:44402983:A:T	E390V	0.999
15:44402984:G:C	E390D	0.999
15:44402984:G:T	E390D	0.999
15:44402988:G:C	D392H	0.999
15:44402989:A:T	D392V	0.999
15:44402991:A:C	K393Q	0.999
15:44402991:A:G	K393E	0.999
15:44402992:A:C	K393T	0.999
15:44402992:A:T	K393M	0.999
15:44402997:G:C	A395P	0.999
15:44289226:G:C	R66P	0.998
15:44289238:T:C	L70P	0.998
15:44402958:G:C	D382H	0.998
15:44402973:G:C	G387R	0.998
15:44402973:G:T	G387C	0.998
15:44402976:G:A	E388K	0.998
15:44402977:A:G	E388G	0.998
15:44402979:T:C	Y389H	0.998
15:44402982:G:A	E390K	0.998

dbSNP variants (sampled 300 via entrez): RS1000020722 (15:44368721 A>G), RS1000042567 (15:44415678 G>C), RS1000073560 (15:44415770 G>A), RS1000116601 (15:44325478 C>G,T), RS1000158323 (15:44385089 A>C,G), RS1000226664 (15:44332678 A>T), RS1000227066 (15:44292360 C>A,G), RS1000273382 (15:44347338 C>G), RS1000308467 (15:44347579 G>A), RS1000312069 (15:44319150 G>T), RS1000325430 (15:44363503 C>A,G), RS1000344485 (15:44382736 T>C), RS1000361405 (15:44334132 G>A,C), RS1000381080 (15:44408280 A>G), RS1000383845 (15:44288830 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST010796_892	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-08
GCST010796_893	Electrocardiogram morphology (amplitude at temporal datapoints)	5.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
FR900359	increases phosphorylation	1
bisphenol A	decreases methylation	1
trichostatin A	affects expression	1
butyraldehyde	decreases expression	1
beta-methylcholine	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Caffeine	decreases phosphorylation	1
Catechin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Hydrogen Peroxide	increases expression	1
Ivermectin	decreases expression	1
Polychlorinated Biphenyls	affects expression	1
Tobacco Smoke Pollution	increases methylation	1
Metribolone	increases expression	1
Cyclosporine	increases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1T6	Abcam HeLa GOLM2 KO	Cancer cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.